The DOI matches its Crossref record; 48 of the 48 references it cites were found in a registry or an index.
Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis
Open accessAbstract
Viral whole-genome sequencing (WGS) provides critical insight into the transmission and evolution of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Long-read sequencing devices from Oxford Nanopore Technologies (ONT) promise significant improvements in turnaround time, portability and cost, compared to established short-read sequencing platforms for viral WGS (e.g., Illumina). However, adoption of ONT sequencing for SARS-CoV-2 surveillance has been limited due to common concerns around sequencing accuracy. To address this, here we perform viral WGS with ONT and Illumina platforms on 157 matched SARS-CoV-2-positive patient specimens and synthetic RNA controls, enabling rigorous evaluation of analytical performance. We report that, despite the elevated error rates observed in ONT sequencing reads, highly accurate consensus-level sequence determination was achieved, with single nucleotide variants (SNVs) detected at >99% sensitivity and >99% precision above a minimum ~60-fold coverage depth, thereby ensuring suitability for SARS-CoV-2 genome analysis. ONT sequencing also identified a surprising diversity of structural variation within SARS-CoV-2 specimens that were supported by evidence from short-read sequencing on matched samples. However, ONT sequencing failed to accurately detect short indels and variants at low read-count frequencies. This systematic evaluation of analytical performance for SARS-CoV-2 WGS will facilitate widespread adoption of ONT sequencing within local, national and international COVID-19 public health initiatives.
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Dinnes, J., Deeks, J. J., Berhane, S., Taylor, M., Adriano, A., Davenport, C., Dittrich, S., Emperador, D., Takwoingi, Y., Cunningham, J., et al. (2021) · Cochrane Database of Systematic Reviews · doi:10.1002/14651858.cd013705.pub2 · Cited by 591
From Omics to Multi-Omics: A Review of Advantages and Tradeoffs
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Metadata
- Authors
- Bull, R. A., Adikari, T. N., Ferguson, J. M., Hammond, J. M., Stevanovski, I., Beukers, A. G., Naing, Z., Yeang, M., Verich, A., Gamaarachchi, H., Kim, K. W., Luciani, F., Stelzer-Braid, S., Eden, J.-S., Rawlinson, W. D., van Hal, S. J., & Deveson, I. W.
- Venue
- Nature Communications
- Published
- 2020-12-09
- Volume
- 11
- Issue
- 1
- Pages
- 6272-6272
- ISSN
- 2041-1723 (ISSN-L)
- OpenAlex
- W3112249938
- Cited by
- 269
- References
- 48
- FWCI
- 12.79
- Type
- journal article
- Language
- en
- Open access
- gold
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- Bull, R. A., Adikari, T. N., Ferguson, J. M., Hammond, J. M., Stevanovski, I., Beukers, A. G., Naing, Z., Yeang, M., Verich, A., Gamaarachchi, H., Kim, K. W., Luciani, F., Stelzer-Braid, S., Eden, J.-S., Rawlinson, W. D., van Hal, S. J., & Deveson, I. W. (2020). Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis. Nature Communications. https://doi.org/10.1038/s41467-020-20075-6
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